Microalgae are ideal candidates for bioremediation and biotechnological applications. However, salinity and nutrient resource availability vary seasonally and between cultivation sites, potentially impacting on biomass productivity. The aim of this study was to screen pollutant-tolerant freshwater microalgae (Desmodesmus armatus, Mesotaenium sp., Scenedesmus quadricauda and Tetraedron sp.), isolated from Tarong power station ash-dam water, for their tolerance to cultivation at a range of salinities. To determine if biochemical composition could be manipulated, the effects of 4-day nutrient limitation were also determined. Microalgae were cultured at 2, 8, 11 and 18 ppt salinity, and nutrient uptake was monitored daily. Growth, total lipid, fatty acid (FA), and amino acid contents were quantified in biomass harvested while nutrient-replete and, after 4 days, nutrient-deplete. D. armatus showed the highest salinity tolerance actively growing in up to 18 ppt while Mesotaenium sp. was the least halotolerant with decreasing growth rates from 11 ppt. However, Mesotaenium sp. at 2 and 8 ppt had the highest biomass productivity and nutrient requirements of the four species, making it ideal for nutrient remediation of eutrophic freshwater effluents. Salinity and nutrient status had minimal influence on total lipid and FA contents in D. armatus and Mesotaenium sp., while nutrient depletion induced an increase of total lipid and FAs in S. quadricauda and Tetraedron sp., which was further increased with increasing salinity. As none of the growth conditions affected amino acid profiles of the species, these findings provide a basis for species selection based on site-specific salinity conditions and nutrient resource availability.